Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae

Advancements in Bacteriophages for the Fire Blight Pathogen Erwinia amylovora

Erwinia amylovora, the causative agent of fire blight, causes significant economic losses for farmers worldwide by inflicting severe damage to the production and quality of plants in the Rosaceae family. Historically, fire blight control has primarily relied on the application of copper compounds and antibiotics, such as streptomycin. However, the emergence of antibiotic-resistant strains and growing environmental concerns have highlighted the need for alternative control methods. Recently, there has been a growing interest in adopting bacteriophages (phages) as a biological control strategy. Phages have demonstrated efficacy against the bacterial plant pathogen E. amylovora, including strains that have developed antibiotic resistance. The advantages of phage therapy includes its minimal impact on microbial community equilibrium, the lack of a detrimental impact on plants and beneficial microorganisms, and its capacity to eradicate drug-resistant bacteria. This review addresses recent advances in the isolation and characterization of E. amylovora phages, including their morphology, host range, lysis exertion, genomic characterization, and lysis mechanisms. Furthermore, this review evaluates the environmental tolerance of E. amylovora phages. Despite their potential, E. amylovora phages face certain challenges in practical applications, including stability issues and the risk of lysogenic conversion. This comprehensive review examines the latest developments in the application of phages for controlling fire blight and highlights the potential of E. amylovora phages in plant protection strategies.

Characteristics and whole-genome analysis of a novel Pseudomonas syringae pv. tomato bacteriophage D6 isolated from a karst cave

Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.

Occurrence of Pseudomonas syringae pvs. actinidiae, actinidifoliorum and Other P. syringae Strains on Kiwifruit in Northern Spain

Pseudomonas syringae pv. actinidiae (Psa), the agent causing bacterial canker of kiwifruit, has been present in the Principality of Asturias (PA), Northern Spain, since 2013, although with restricted distribution. In this study, 53 strains collected in kiwifruit orchards in PA during the period 2014-2020 were characterized by a polyphasic approach including biochemical and phylogenetic analysis. Thirty-three strains, previously identified by PCR as Psa, have been found to be a homogeneous group in phylogenetic analysis, which seems to indicate that there have been few introductions of the pathogen into the region. Two strains were confirmed as P. syringae pv. actinidifoliorum (Pfm), so this is the first report of Pfm in the PA. The remaining 18 strains were found to be close to P. avellanae and P. syringae pv. antirrhini or to strains described as Pfm look-alikes. Pathogenicity tests carried out on peppers with a selection of strains have shown that both Psa and Pfm caused clear damage, while the 18 atypical strains caused variable lesions. It would be necessary to carry out pathogenicity testing of atypical strains on kiwifruit plants to study the role of these strains in the kiwifruit pathosystem to evaluate their pathogenic potential in this crop.

Genome sequences of Mx1, the first Myxococcus phage isolated, and Mx4, a generalized transducing myxophage

Myxococcus xanthus is the best-studied member of the phylum Myxococcota, but the bacteriophages infecting it and their characterization remain limited. Here, we present complete genomes of Mx1, the first Myxococcus phage isolated, and of an Mx4 derivative widely used for generalized transduction, both unclassified Caudoviricetes with long, contractile tails.

Genomic and proteomic characterization of vB_SauM-UFV_DC4, a novel Staphylococcus jumbo phage

Staphylococcus aureus is one of the most relevant mastitis pathogens in dairy cattle, and the acquisition of antimicrobial resistance genes presents a significant health issue in both veterinary and human fields. Among the different strategies to tackle S. aureus infection in livestock, bacteriophages have been thoroughly investigated in the last decades; however, few specimens of the so-called jumbo phages capable of infecting S. aureus have been described. Herein, we report the biological, genomic, and structural proteomic features of the jumbo phage vB_SauM-UFV_DC4 (DC4). DC4 exhibited a remarkable killing activity against S. aureus isolated from the veterinary environment and stability at alkaline conditions (pH 4 to 12). The complete genome of DC4 is 263,185 bp (GC content: 25%), encodes 263 predicted CDSs (80% without an assigned function), 1 tRNA (Phe-tRNA), multisubunit RNA polymerase, and an RNA-dependent DNA polymerase. Moreover, comparative analysis revealed that DC4 can be considered a new viral species belonging to a new genus DC4 and showed a similar set of lytic proteins and depolymerase activity with closely related jumbo phages. The characterization of a new S. aureus jumbo phage increases our understanding of the diversity of this group and provides insights into the biotechnological potential of these viruses. KEY POINTS: • vB_SauM-UFV_DC4 is a new viral species belonging to a new genus within the class Caudoviricetes. • vB_SauM-UFV_DC4 carries a set of RNA polymerase subunits and an RNA-directed DNA polymerase. • vB_SauM-UFV_DC4 and closely related jumbo phages showed a similar set of lytic proteins.

Advancements in the Use of Bacteriophages to Combat the Kiwifruit Canker Phytopathogen Pseudomonas syringae pv. actinidiae

Over the last several decades, kiwifruit production has been severely damaged by the bacterial plant pathogen Pseudomonas syringae pv. actinidiae (Psa), resulting in severe economic losses worldwide. Currently, copper bactericides and antibiotics are the main tools used to control this bacterial disease. However, their use is becoming increasingly ineffective due to the emergence of antibiotic resistance. In addition, environmental issues and the changes in the composition of soil bacterial communities are also concerning when using these substances. Although biocontrol methods have shown promising antibacterial effects on Psa infection under in vitro conditions, the efficiency of antagonistic bacteria and fungi when deployed under field conditions remains unclear. Therefore, it is crucial to develop a phage-based biocontrol strategy for this bacterial pathogen. Due to the specificity of the target bacteria and for the benefit of the environment, bacteriophages (phages) have been widely regarded as promising biological agents to control plant, animal, and human bacterial diseases. An increasing number of studies focus on the use of phages for the control of plant diseases, including the kiwifruit bacterial canker. In this review, we first introduce the characteristics of the Psa-induced kiwifruit canker, followed by a description of the diversity and virulence of Psa strains. The main focus of the review is the description of recent advances in the isolation of Psa phages and their characterization, including morphology, host range, lytic activity, genome characterization, and lysis mechanism, but we also describe the biocontrol strategies together with potential challenges introduced by abiotic factors, such as high temperature, extreme pH, and UV irradiation in kiwifruit orchards. The information presented in this review highlights the potential role of phages in controlling Psa infection to ensure plant protection.

A lipopolysaccharide-dependent phage infects a pseudomonad phytopathogen and can evolve to evade phage resistance

Bacterial pathogens are major causes of crop diseases, leading to significant production losses. For instance, kiwifruit canker, caused by the phytopathogen Pseudomonas syringae pv. actinidiae (Psa), has posed a global challenge to kiwifruit production. Treatment with copper and antibiotics, whilst initially effective, is leading to the rise of bacterial resistance, requiring new biocontrol approaches. Previously, we isolated a group of closely related Psa phages with biocontrol potential, which represent environmentally sustainable antimicrobials. However, their deployment as antimicrobials requires further insight into their properties and infection strategy. Here, we provide an in-depth examination of the genome of ΦPsa374-like phages and show that they use lipopolysaccharides (LPS) as their main receptor. Through proteomics and cryo-electron microscopy of ΦPsa374, we revealed the structural proteome and that this phage possess a T = 9 capsid triangulation, unusual for myoviruses. Furthermore, we show that ΦPsa374 phage resistance arises in planta through mutations in a glycosyltransferase involved in LPS synthesis. Lastly, through in vitro evolution experiments we showed that phage resistance is overcome by mutations in a tail fibre and structural protein of unknown function in ΦPsa374. This study provides new insight into the properties of ΦPsa374-like phages that informs their use as antimicrobials against Psa.

Genomes within genomes: nested symbiosis and its implications for plant evolution

Many important plant traits are products of nested symbiosis: mobile genetic elements (MGEs) are nested within microbes, which in turn, are nested within plants. Plant trait variation is therefore not only determined by the plant's genome, but also by loci within microbes and MGEs. Yet it remains unclear how interactions and coevolution within nested symbiosis impacts the evolution of plant traits. Despite the complexities of nested symbiosis, including nonadditive interactions, understanding the evolution of plant traits is facilitated by combining quantitative genetic and functional genomic approaches that explicitly consider sources of nested genetic variation (from loci in MGEs to microbiomes). Additionally, understanding coevolution within nested symbiosis enables us to design or select for MGEs that promote plant health.

The Bacteriophage Pf-10-A Component of the Biopesticide "Multiphage" Used to Control Agricultural Crop Diseases Caused by Pseudomonas syringae

Phytopathogenic pseudomonads are widespread in the world and cause a wide range of plant diseases. In this work, we describe the Pseudomonas phage Pf-10, which is a part of the biopesticide "Multiphage" used for bacterial diseases of agricultural crops caused by Pseudomonas syringae. The Pf-10 chromosome is a dsDNA molecule with two direct terminal repeats (DTRs). The phage genomic DNA is 39,424 bp long with a GC-content of 56.5%. The Pf-10 phage uses a packaging mechanism based on T7-like short DTRs, and the length of each terminal repeat is 257 bp. Electron microscopic analysis has shown that phage Pf-10 has the podovirus morphotype. Phage Pf-10 is highly stable at pH values from 5 to 10 and temperatures from 4 to 60 °C and has a lytic activity against Pseudomonas strains. Phage Pf-10 is characterized by fast adsorption rate (80% of virions attach to the host cells in 10 min), but has a relatively small number of progeny (37 ± 8.5 phage particles per infected cell). According to the phylogenetic analysis, phage Pf-10 can be classified as a new phage species belonging to the genus Pifdecavirus, subfamily Studiervirinae, family Autographiviridae, order Caudovirales.

Emerging Aspects of Jumbo Bacteriophages

The bacteriophages have been explored at a huge scale as a model system for their applications in many biological-related fields. Jumbo phages with a large genome size from 200 to 500 kbp were not previously assigned a great value, and characterized by complex structures coupled with large virions with a wide variety of hosts. The origin of most of the jumbo phages was not well understood; however, many other prominent features have been discovered recently. In the current review, we strive to unearth the most advanced characteristics of jumbo phages, particularly their significance and structural organization that holds immense value to the viral life cycle. The unique characteristics of jumbo phages are the basis of variations in different types of phages concerning their organization at the genomic level, virion structure, evolution, and progeny propagation. The presence of tRNA and additional translation-related genes along with chaperonin genes mark the ability of these phages for being independent of host molecular machinery enabling them to have wide host options. A large number of jumbo phages have been isolated from various sources through advanced standard screening methods. The current review has summarized the available data on jumbo phages and discussed the genome orientation of jumbo phages, translational machinery, diversity and evolution of jumbo phages. In the studies conducted, jumbo phages possessed special additional genes that helps to reduce the dependence of jumbo phages on their hosts. Furthermore, their genomes might have evolved from smaller genome phages.

Molecular Characterization and Taxonomic Assignment of Three Phage Isolates from a Collection Infecting Pseudomonas syringae pv. actinidiae and P. syringae pv. phaseolicola from Northern Italy

Bacterial kiwifruit vine disease (Pseudomonas syringae pv. actinidiae, Psa) and halo blight of bean (P. syringae pv. phaseolicola, Pph) are routinely treated with copper, leading to environmental pollution and bacterial copper resistance. An alternative sustainable control method could be based on bacteriophages, as phage biocontrol offers high specificity and does not result in the spread of toxic residues into the environment or the food chain. In this research, specific phages suitable for phage-based biocontrol strategies effective against Psa and Pph were isolated and characterized. In total, sixteen lytic Pph phage isolates and seven lytic Psa phage isolates were isolated from soil in Piedmont and Veneto in northern Italy. Genome characterization of fifteen selected phages revealed that the isolated Pph phages were highly similar and could be considered as isolates of a novel species, whereas the isolated Psa phages grouped into four distinct clades, two of which represent putative novel species. No lysogeny-, virulence- or toxin-related genes were found in four phages, making them suitable for potential biocontrol purposes. A partial biological characterization including a host range analysis was performed on a representative subset of these isolates. This analysis was a prerequisite to assess their efficacy in greenhouse and in field trials, using different delivery strategies.

Intracellular Organization by Jumbo Bacteriophages

Since their discovery more than 100 years ago, the viruses that infect bacteria (bacteriophages) have been widely studied as model systems. Largely overlooked, however, have been "jumbo phages," with genome sizes ranging from 200 to 500 kbp. Jumbo phages generally have large virions with complex structures and a broad host spectrum. While the majority of jumbo phage genes are poorly functionally characterized, recent work has discovered many unique biological features, including a conserved tubulin homolog that coordinates a proteinaceous nucleus-like compartment that houses and segregates phage DNA. The tubulin spindle displays dynamic instability and centers the phage nucleus within the bacterial host during phage infection for optimal reproduction. The shell provides robust physical protection for the enclosed phage genomes against attack from DNA-targeting bacterial immune systems, thereby endowing jumbo phages with broad resistance. In this review, we focus on the current knowledge of the cytoskeletal elements and the specialized nuclear compartment derived from jumbo phages, and we highlight their importance in facilitating spatial and temporal organization over the viral life cycle. Additionally, we discuss the evolutionary relationships between jumbo phages and eukaryotic viruses, as well as the therapeutic potential and drawbacks of jumbo phages as antimicrobial agents in phage therapy.

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.

Characterization of Bacteriophages against Pseudomonas Syringae pv. Actinidiae with Potential Use as Natural Antimicrobials in Kiwifruit Plants

Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of a bacterial canker in kiwifruit plants and has caused economic losses worldwide. Currently, the primary strategies to control this pathogen include the use of copper-based compounds and even antibiotics. However, the emergence of isolates of Psa that are resistant to these agrochemicals has raised the need for new alternatives to control this pathogen. Bacteriophages have been proposed as an alternative to control bacterial infections in agriculture, including Psa. Here, we show the isolation and characterization of 13 phages with the potential to control Psa infections in kiwifruit plants. The phages were characterized according to their host range and restriction fragment length polymorphism (RFLP) pattern. Four phages were selected according to their lytic effect on the bacteria and their tolerance to different environmental conditions of pH (4–7), temperature (4–37 °C), and solar radiation exposure (30 and 60 min). The selected phages (CHF1, CHF7, CHF19, and CHF21) were sequenced, revealing a high identity with the podophage of Psa phiPSA2. In vitro assays with kiwifruit leaf samples demonstrated that the mixture of phages reduced the Psa bacterial load within three hours post-application and was able to reduce the damage index in 50% of cases. Similarly, assays with kiwifruit plants maintained in greenhouse conditions showed that these phages were able to reduce the Psa bacterial load in more than 50% of cases and produced a significant decrease in the damage index of treated plants after 30 days. Finally, none of the selected phages were able to infect the other bacteria present in the natural microbiota of kiwifruit plants. These results show that bacteriophages are an attractive alternative to control Psa infections in kiwifruit plants.